small changes in gapfill #52

draeger-lab · Nov 11, 2024 · 15d0de7 · 15d0de7
1 parent 459506d
commit 15d0de7
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/src/refinegems/classes/gapfill.py b/src/refinegems/classes/gapfill.py
@@ -1808,7 +1808,7 @@ def find_missing_reactions(self, model:cobra.Model,
         self.missing_genes = updated_missing_genes
         self.missing_reactions = mapped_reacs
 
-        self._statistics['reactions']['missing (before)'] = len(self.missing_reactions)
+        self._statistics['reactions']['missing (before)'] = len(self.missing_reactions) + self._statistics['reactions']['missing information']
 
 
 

diff --git a/src/refinegems/utility/connections.py b/src/refinegems/utility/connections.py
@@ -183,11 +183,11 @@ def run_DIAMOND_blastp(fasta:str, db:str,
     """
 
     if outdir:
-        outname = Path(outdir,'DIAMOND_blastp_res.tsv')
-        logfile = Path(outdir,'log_DIAMOND_blastp.txt')
+        outname = str(Path(outdir,'DIAMOND_blastp_res.tsv'))
+        logfile = str(Path(outdir,'log_DIAMOND_blastp.txt'))
     else:
-        outname = Path(outname)
-        logfile = Path('log_DIAMOND_blastp.txt')
+        outname = str(Path(outname))
+        logfile = str(Path('log_DIAMOND_blastp.txt'))
 
     # @TODO: test, if it works with different paths and their problems  
     subprocess.run(['diamond', 'blastp', '-d', db, '-q', fasta, '--'+sensitivity, '--query-cover', str(coverage), '-p', str(threads), '-o', outname, '--outfmt', str(6), 'qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore', '2>', logfile], shell=True)